help > RE: Denoised data
Feb 18, 2016  03:02 PM | Alfonso Nieto-Castanon - Boston University
RE: Denoised data
Hi Bob,

Yes, the niftiDATA_Subject*_Condition000.nii file will contain the entire functional data for this subject (concatenated across multiple sessions). In relatively recent versions of conn we are no longer explicitly breaking the data into condition-specific sub-datasets, but rather keeping the entire data in a single file (in this case the in DATA_Subject001_Condition000.matc file) and then including explicit references to the specific scans and scan-weights associated with each condition (in this case in the DATA_Subject001_Condition001.mat and DATA_Subject001_Condition002.mat fles). This change was introduced when we added gPPI analyses to CONN (while weighted-GLM analyses work perfectly fine with just the condition-specific denoised sub-datasets, PPI analyses require the entire denoised data to be modeled). When converting these files to nifti format only the *Condition000 files will be converted to their associated .nii files. If you want to split this into the original session-specific portions, I would probably suggest to use spm_file_merge for that (see for example this post http://www.nitrc.org/forum/message.php?msg_id=14106 for specific instructions)

Hope this helps
Alfonso

Originally posted by Bob Kraft:
I am saving the denoised data to a NIFTI file.  I have two conditions acquired during two separate sessions.  Each fMRI data set has 190 volumes. 
I found the data in the folder conn/results/preprocessing.  The files in this directory are


BETA_denoising_Subject001.nii
DATA_Subject001_Condition000.matc
DATA_Subject001_Condition001.mat
DATA_Subject001_Condition002.mat
_list_BETA_denoising.mat
_list_BETA_denoising.txt
_list_conditions.mat
niftiDATA_Subject001_Condition000.nii
ROI_Subject001_Condition000.mat
ROI_Subject001_Condition001.mat
ROI_Subject001_Condition002.mat
vvPCeig_Subject001_Condition001.log
vvPCeig_Subject001_Condition001.mat
vvPCeig_Subject001_Condition002.log
vvPCeig_Subject001_Condition002.mat
vvPC_Subject001_Condition001.mat
vvPC_Subject001_Condition001.matc
vvPC_Subject001_Condition002.mat
vvPC_Subject001_Condition002.matc

You can see that there are three conditions located in the directory  (Conditions000, Conditions001, and Conditions002).  
The only nifti files located in this directory are

BETA_denoising_Subject001.nii
niftiDATA_Subject001_Condition000.nii

The niftiData_Subject000_Condition000.nii contains 380 volumes (=2*190).  I would like to confirm that the denoised data for both conditions have been concatenated together and are stored in this file.

If this is the case, I would also like to know is there a reason why the two separate denoised runs were concatenated together.  

Thanks

Bob

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TitleAuthorDate
Bob Kraft Feb 15, 2016
RE: Denoised data
Alfonso Nieto-Castanon Feb 18, 2016